Molecular dynamics simulation of the hydration of adenosine phosphates

Abstract

The hydration behavior of adenosine triphosphate (ATP), adenosine diphosphate (ADP), and adenosine monophosphate (AMP) has been investigated with molecular dynamics simulations. The spatial distribution of water molecules around different hydration sites of the adenosine phosphates and the average times that water molecules spend in the vicinity of the hydration sites of the phosphate, ribose, and adenine groups have been examined in order to characterize the hydration extent of different regions of the ATP, ADP, and AMP molecules. The water molecules strongly hydrate the negatively-charged phosphate groups of the adenosine phosphates and the interaction between the oxygen and nitrogen atoms of the ribose and adenine rings with water molecules lead to the full hydration of these groups by the water molecules as well. The adenosine phosphates ATP, ADP, and AMP were found to be fully hydrated by the water molecules regardless of the magnitude of their negative charges. Results of this work provide atomic-level information about the hydration of ATP, ADP, and AMP were and are expected to help better understand the behavior of these molecules in biological systems.